I am relatively new to Xcode and one thing that has bothered me is that when I add a resource it gets added to the top level directory of my project directory. So for exampl
Here's a little more explanation of Graham's suggestion:
Now, anything you put in the images group will automatically go into the images directory. That's true if you drag/drop from within Xcode, from other other projects or from Finder, or if you Add New... by right-clicking on the images directory. (This assumes you leave the default setting of "relative to group" in the info pane.)
This will work for anything you put in that group (NIBs, etc).
For imageNamed:, you just give the base name.
My recommendation is to keep a small number of filesystem directories, and mostly organize with groups in Xcode. But I agree, a small number of filesystem directories are very helpful. I put all my source code in a Classes directory (just because Apple used that name; I would have picked "Sources" or something). I also have a Resources directory at the top level and generally create images and audio directories under that. But I don't generally create a lots of real directories beyond that. This keeps things a bit tidier, but makes it easier to grep and wildcard things with the shell.
Beyond shell tools, the big advantage of organizing by groups rather than directories is the impact on version control systems like subversion. When you suddenly realize that your "Views" group is way too big, you can reorganize it without taking the huge impact of moving files around.